Homology Modeling

Limitations of Experimental Methods

Annotated proteins in the databank: ~ 100,000

Proteins with known structure: ~5,000 !

Total number including ORFs: ~ 700,000

Protein modeling Provide a solid basis for,

structure-based drug design

analysis of protein function, interactions, antigenic behavior

rational design of proteins with increased stability or novel functions

Homology ModelingBased on two major observations:

1) The structure of a protein is determined by its amino acid sequence

2) Structure is much more conserved than sequence during evolution

What’s homology modeling?

Predicts the three-dimensional structure of a given protein sequence (target) based on an alignment to one or more known protein structures (templates).

If similarity between the target sequence and the template sequence is detected, structural similarity can be assumed.

In general, 30% sequence identity is required to generate an useful model.

Accuracy and application of protein structure

Does sequence similarity implies structure similarity?

Safe Zone

Twilight Zone

Structure prediction by homology modeling

In summary: homology modeling steps1) Template recognition & initial alignment2) Alignment correction3) Backbone generation4) Loop modeling5) Side-chain modeling6) Model optimization7) Model validation

Steps in Homology Modeling

Step 1: Template Recognition and Initial Alignment:-

In practice, one just feeds the query sequence to one of the countless BLAST servers on the web, selects a search of the PDB, and obtains a list of hits—the modeling templates and corresponding alignments

BLAST Basic Local Alignment Search Tool

Most widely used bioinformatics program

Emphasizes speed over sensitivity (speed is vital to making the algorithm practical on the huge genome databases)

Overview - METABOLISM

Sites of biotransformation where ever appropriate enzymes occur; plasma,

kidney, lung, gut wall and

LIVER

the liver is ideally placed to intercept natural ingested toxins (bypassed by injections etc) and has a major role in biotransformation

1.Residue exchange matrix

2. An alignment matrix

By comparing thousands of sequences and sequence families, it became clear that the opening of gapsis about as unlikely as at least a couple of nonidentical residues in a row.

Opening penalty: for every new gap

Gap extension penalty: for every residue that is skippedin the alignment

Step 2: Alignment Correction

Sometimes it may be difficult to align two sequences in a region where the percentagesequence identity is very low.

One can then use other sequences from homologous proteins to find a solution.

LTLTLTLT

YAYAYAYAVY

TYTYTYTYT TYTYTYTYT−LTLTLTLT−

−YAYAYAYAY

2 is correct, because it leads to a small gap, compared to a huge hole associated with alignment 1.

TemplateSequence 17

115

97.5 Å

1.3 Å

Step 3: Backbone Generation:-

One simply copies the coordinates of those template residues that show up in the alignment with the model sequence.

If two aligned residues differ, only the backbone coordinates (N,Cα,C and O) can be copied.

If they are the same, one can also include the side chain.

Step 4: Loop Modeling:-

There are two main approaches to loop modeling:-1). Knowledge based: one searches the PDB for known loops with endpoints that match the residues between which the loop has to be inserted and simply copies the loop conformation.2). Energy based: as in true ab initio fold prediction, an energy function is used to judge the quality of a loop

Step 5: Side-Chain Modeling:-

Comparing the side-chain conformations (rotamers) of residues that are conserved in structurally similar proteins

Similar torsion angle about the Cα −Cβ bond - It is therefore possible to simply copy conserved residues entirely from the template to the model

Step 6: Model Optimization:- Energy = Stretching Energy +Bending Energy +Torsion Energy +Non-Bonded Interaction Energy

Step 7: Model Validation

Model should be evaluated for:

- correctness of the overall fold/structure

- errors over localized regions

- stereochemical parameters: bond lengths, angles, etc

Step 7: Model Validation

QUESTIONS?????

B.Satish Kumar M.Tech (bio-tech) JNTU

Thank You